Joachim Wolff

Reply to: Reply to: False positives in the study of memory-related gene expression In the Nature paper “Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory” published on March 14th, 2024, authors Sun et al. claimed to identify cell-type specifi…

I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...

This is very interesting!

(1/n) New preprint from @claricehongky.bsky.social
Fan Fang Varshini Ramanathan in collab w Jie Liu.

Q: How do we get ultra-high-res 3D genome maps?

A: New deep learning model, Cleopatra.

Cleo trains on Micro-C, fine-tunes on RCMC, and predicts genome-wide 3D maps at ultra-high resolution.

Always on the Move: Overview on Chromatin Dynamics within Nuclear Processes Our genome is organized into chromatin, a dynamic and modular structure made of nucleosomes. Chromatin organization controls access to the DNA sequence, playing a fundamental role in cell identity and...

Want to learn more about chromatin and its dynamics? Read this review by Charlotte and Jolijn in our lab, aimed at giving an overview on this and the ways this is dealt with during transcription, replication and damage repair. Thanks to Biochemistry for inviting us! doi.org/10.1021/acs....

AI-driven discovery of synergistic drug combinations against pancreatic cancer - Nature Communications Finding optimal multi-drug combinations for pancreatic cancer remains a complex task. Here, authors across three different groups apply machine learning approaches to predict synergy across 1.6 millio...

AI-driven discovery of synergistic drug combinations against pancreatic cancer 🧪 🧬🖥️ www.nature.com/articles/s41...

A call for built-in biosecurity safeguards for generative AI tools - Nature Biotechnology Nature Biotechnology - A call for built-in biosecurity safeguards for generative AI tools

A call for built-in biosecurity safeguards for generative AI tools go.nature.com/3GIpTlR

Biolearn Biolearn enables easy and versatile analyses of biomarkers of aging data. It provides tools to easily load data from publicly available sources like the Gene Expression Omnibus, National Health and...

The Biomarkers of Aging Consortium would like feedback on its tool Biolearn, which is used for analyses of aging biomarkers data. See the links below to Biolearn and the survey:

bio-learn.github.io
tally.so/r/wovVQO

MYC and AP-1 oncogenes synergistically bind enhancers to rewire transcription https://www.biorxiv.org/content/10.1101/2025.04.28.650480v1

Exclusive: the most-cited papers of the twenty-first century A Nature analysis reveals the 25 highest-cited papers published this century and explores why they are breaking records.

The most-cited papers of the twenty-first century so far include those that describe developments in AI; approaches to improve the quality of research or systematic reviews; cancer statistics & research software
@nature.com
🧪

www.nature.com/articles/d41...

YouTube video by Johan Gibcus Rules of Engagement

Earnshaw, Goloborodko, Dekker & Mirny labs are excited to present our latest work, "Rules of engagement for condensins and cohesins guide mitotic chromosome formation" - now accepted!!
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...

Epigenetics and individuality: from concepts to causality across timescales - Nature Reviews Genetics Recent genomic approaches are providing unprecedented opportunity to disentangle how genotype and environment affect organismal traits. The authors review the role of epigenetic variation in mediating...

Review | Epigenetics and individuality: from concepts to causality across timescales www.nature.com/articles/s41...

Google Makes New Quantum Computing Breakthrough Google unveiled an experimental machine capable of tasks that a traditional supercomputer could not master in 10 septillion years. (That’s older than the universe.)

Quantum Computing Inches Closer to Reality After Another Google Breakthrough

Google unveiled an experimental machine capable of tasks that a traditional supercomputer could not master in 10 septillion years. (That’s older than the universe.)

www.nytimes.com/2024/12/09/t...

By definition, enhancers can activate from a distance. But with increased distance between enhancer and promoter, the activation drops. To study this systematically, we build a synthetic locus: www.cell.com/molecular-ce... 1/12

After we reach advanced age, around 80, the propensity to develop cancer is markedly reduced. A discovery reported at Nature today about aged stem cells and iron insufficiency may help explain this advantage

www.nature.com/articles/d41...

Targeting chromatin modifying complexes in acute myeloid leukemia Abstract. Acute myeloid leukemia (AML) is a devastating hematologic malignancy with high rates of relapse, which can, in part, be attributed to the dysregu

Overwhelmed by all of the exciting new research on chromatin modifiers in AML? Find it hard to keep track of all the new menin inhibitors? Well good news, we’ve just published the perfect review for you in SCTM!

@alexkschurer.bsky.social
@gritsmanlab.bsky.social

academic.oup.com/stcltm/advan...

Enhancer cooperativity can compensate for loss of activity over large genomic distances Thomas, Feng, et al. introduce a synthetic platform that allows the building of complex regulatory landscapes. Integrating the same enhancer at different distances from a promoter uncovered that activ...

Enhancer cooperativity can compensate for loss of activity over large genomic distances www.cell.com/molecular-ce...

A Scaffolding Element Rewires Local 3D Chromatin Architecture During Differentiation Upon differentiation chromatin rewires to reflect its new cellular identity and function. While it is widely known that this process involves cooperative changes in transcription, chromatin compositio...

Thank you for the comment and letting me know for the link. Here it is: www.biorxiv.org/content/10.1...

Emerging roles of cohesin-STAG2 in cancer - Oncogene Oncogene - Emerging roles of cohesin-STAG2 in cancer

Honoured to be invited for the Emerging Leaders Edition of Oncogene! This review, spearheaded by my postdoc Julia Scott, explores cohesin-STAG2’s roles in chromatin architecture, transcriptional regulation, and cancer biology. Read it here: www.nature.com/articles/s41...

Transposable element 5mC methylation state of blood cells predicts age and disease - Nature Aging https://www.nature.com/articles/s43587-024-00757-2

Enhanced SNP Genotyping with Symmetric Multinomial Logistic Regression https://www.biorxiv.org/content/10.1101/2024.11.28.625807v1 In genotyping, determining Single Nucleotide Polymorphisms (SNPs) is standard practice, but it becom

Enhanced SNP Genotyping with Symmetric Multinomial Logistic Regression https://www.biorxiv.org/content/10.1101/2024.11.28.625807v1

A panoramic view of cell population dynamics in mammalian aging To elucidate aging-associated cellular population dynamics, we present PanSci, a single-cell transcriptome atlas profiling over 20 million cells from 623 mouse tissues across different life stages, se...

Excited to share our work @science.org. led by our incredible @tommyz626.bsky.social at @rockefelleruniv.bsky.social! By profiling 21 million single cells across life stages, we reveal aging as distinct, development-like transitions, with dramatic cell population changes in specific time windows!

Evolution and function of chromatin domains across the tree of life - Nature Structural & Molecular Biology Szalay et al. discuss cross-kingdom similarities and differences in 3D chromatin folding in relation to gene regulation, including in bacteria, archaea, mammals and plants. This comparison reveals cer...

🔺🔺🔺RED TRIANGLE ALERT 🔺🔺🔺
Ever wonder how #TADs compare across the tree of life?Look no further & read our Review!!!

Find out what genes & 3D chromatin can & can't do in Bacteria! Archeae! Yeast! Plants! Animals!

SMCs & RNA-Pol are the only thing they have in common
www.nature.com/articles/s41...

Generalized AI models for genomics applications - Nature Methods The Nucleotide Transformer is a series of foundation models pre-trained on DNA sequences through self-supervised learning that extracts context-specific representations of nucleotide sequences. These ...

Generalized AI models for genomics applications www.nature.com/articles/s41...

🔖New paper from the lab!
'Evolution of 3D Chromatin Folding' | Annual Reviews - go.shr.lc/3B60kZF

Would love to be entered. One bioinformatics core person :)

ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...

One enhancer can activate two endogenous genes simultaneously and across a TAD Boundary. Check out our new preprint.
www.biorxiv.org/content/10.1...

@raduzabet.bsky.social can you add me to the epigenetics and chromatin starter pack? Thanks!

This is amazing article! Thanks
@erictopol.bsky.social
for highlighting two of our new foundation models for DNA methylation!

Transient histone deacetylase inhibition induces cellular memory of gene expression and three-dimensional genome folding Epigenetic memory enables the stable propagation of gene expression patterns in response to transient developmental and environmental stimuli. Although three-dimensional (3D) organisation is emerging ...

Exciting weekend read from G Cavailli's lab, on how histone acetylation turnover shapes 3D genome folding and transcriptional memory

+ Deepest micro-C ever in mESCs 😲 + Protocol updates for reducing coverage biases of micro-C 🤔

www.biorxiv.org/content/10.1...